There's definitely some solid concepts in here!
In the end, I did fight Kronii in the Throne of Eons and I spent my time maxing out all of the upgrade tree before fighting her. It admittedly made the Kronii fight quick work... though I personally like that taking the time to max everything out actually has you feel strong though (similar to how finishing all the side-quests in a typical RPG is bound to leave you overleveled for the final boss). Maybe there'd be some fine tuning to not make the final boss a cakewalk but still... feeling strong after grinding is a nice feeling.
What I would personally say is I am most fond of are the types of enemies that there are. There's only the melee, the ranged, and the shield/tank... but that's enough of building blocks to create more unique encounters in a longer game with more levels. I already felt a bit of that when I got lucky with some of the randomization gave me something like a couple of shield enemies with a ranged enemy behind 'em.
One thing I wasn't fond though was, in a way, the anti-synergy of gaining more time reducing the rewards I would get. I know the initial mechanic of staying later to get more rewards was meant to be a risk/reward kind of deal, but then gaining time just felt like it punished me when I got to the point where I was able to clear out as much as I could see on the map and then I just sat waiting until I estimated I'd get at least 1.8x the rewards when leaving through a distortion. In the end though, that's just how I personally feel.
So unless I missed something, there's only the Timeswept Graveyard and the Throne of Eons so I think I got through all the game has to offer. And overall, I enjoyed my 20 minutes with the game!